In The Elder Scrolls V: Skyrim, one of the Mage's in the Collage of Winterhold when asked about Necromancy being despised by the Nords says something like
Those Arcanic views vanished along with the Mage's Guild. Necromancy, like any other magic, is a tool to be used.
From my point of view the Collage of Winter Hold serves as the Mage's Guild and the Companions serves as the Fighter's Guild in Skyrim however from what i remember both the Mage's and Fighter's Guilds in Morrowind and Oblivion were more Tamrial (or at least Empire) wide organizations so they should have had Guilds in Skyrim.
since the Thieves Guild and the Dark Brotherhood are still in operation in Skyrim i am wondering what happened to the Mage's and Fighter's Guilds in the 200 years since the end of the 3rd era (the end of the Oblivion Crisis), are they just gone from Skyrim or gone from the world?